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Items: 1 to 50 of 59

1.

Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges.

Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM.

Genome Med. 2019 Jul 25;11(1):45. doi: 10.1186/s13073-019-0660-8. Review.

2.

Extensive global movement of multidrug-resistantM. tuberculosis strains revealed by whole-genome analysis.

Cohen KA, Manson AL, Abeel T, Desjardins CA, Chapman SB, Hoffner S, Birren BW, Earl AM.

Thorax. 2019 Sep;74(9):882-889. doi: 10.1136/thoraxjnl-2018-211616. Epub 2019 May 2.

3.

Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans.

Reddy KC, Dror T, Underwood RS, Osman GA, Elder CR, Desjardins CA, Cuomo CA, Barkoulas M, Troemel ER.

PLoS Pathog. 2019 Jan 14;15(1):e1007528. doi: 10.1371/journal.ppat.1007528. eCollection 2019 Jan.

4.

SynerClust: a highly scalable, synteny-aware orthologue clustering tool.

Georgescu CH, Manson AL, Griggs AD, Desjardins CA, Pironti A, Wapinski I, Abeel T, Haas BJ, Earl AM.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000231. Epub 2018 Nov 12.

5.

Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators.

Hommel B, Mukaremera L, Cordero RJB, Coelho C, Desjardins CA, Sturny-Leclère A, Janbon G, Perfect JR, Fraser JA, Casadevall A, Cuomo CA, Dromer F, Nielsen K, Alanio A.

PLoS Pathog. 2018 May 18;14(5):e1006982. doi: 10.1371/journal.ppat.1006982. eCollection 2018 May.

6.

Advances in Cryptococcus genomics: insights into the evolution of pathogenesis.

Cuomo CA, Rhodes J, Desjardins CA.

Mem Inst Oswaldo Cruz. 2018;113(7):e170473. doi: 10.1590/0074-02760170473. Epub 2018 Feb 19. Review.

7.

Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.

Rhodes J, Desjardins CA, Sykes SM, Beale MA, Vanhove M, Sakthikumar S, Chen Y, Gujja S, Saif S, Chowdhary A, Lawson DJ, Ponzio V, Colombo AL, Meyer W, Engelthaler DM, Hagen F, Illnait-Zaragozi MT, Alanio A, Vreulink JM, Heitman J, Perfect JR, Litvintseva AP, Bicanic T, Harrison TS, Fisher MC, Cuomo CA.

Genetics. 2017 Sep;207(1):327-346. doi: 10.1534/genetics.117.203836. Epub 2017 Jul 5.

8.

Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans.

Desjardins CA, Giamberardino C, Sykes SM, Yu CH, Tenor JL, Chen Y, Yang T, Jones AM, Sun S, Haverkamp MR, Heitman J, Litvintseva AP, Perfect JR, Cuomo CA.

Genome Res. 2017 Jul;27(7):1207-1219. doi: 10.1101/gr.218727.116.

9.

Antagonistic regulation of cell-cycle and differentiation gene programs in neonatal cardiomyocytes by homologous MEF2 transcription factors.

Desjardins CA, Naya FJ.

J Biol Chem. 2017 Jun 23;292(25):10613-10629. doi: 10.1074/jbc.M117.776153. Epub 2017 May 4.

10.

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE 3rd, Brand J; TBResist Global Genome Consortium, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM.

Nat Genet. 2017 Mar;49(3):395-402. doi: 10.1038/ng.3767. Epub 2017 Jan 16.

11.

Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.

Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, Colombo AL, Calvo B, Cuomo CA, Desjardins CA, Berkow EL, Castanheira M, Magobo RE, Jabeen K, Asghar RJ, Meis JF, Jackson B, Chiller T, Litvintseva AP.

Clin Infect Dis. 2017 Jan 15;64(2):134-140. doi: 10.1093/cid/ciw691. Epub 2016 Oct 20. Erratum in: Clin Infect Dis. 2018 Aug 31;67(6):987.

12.

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

Wollenberg KR, Desjardins CA, Zalutskaya A, Slodovnikova V, Oler AJ, Quiñones M, Abeel T, Chapman SB, Tartakovsky M, Gabrielian A, Hoffner S, Skrahin A, Birren BW, Rosenthal A, Skrahina A, Earl AM.

J Clin Microbiol. 2017 Feb;55(2):457-469. doi: 10.1128/JCM.02116-16. Epub 2016 Nov 30.

13.

Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.

Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CM, Teixeira MM, Taylor JW, Clay OK, McEwen JG, Cuomo CA.

mSphere. 2016 Sep 28;1(5). pii: e00213-16. eCollection 2016 Sep-Oct.

14.
15.

Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis.

Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6600-6608. doi: 10.1128/AAC.00664-16. Print 2016 Nov.

16.

Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors.

Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT.

Cell Chem Biol. 2016 Jun 23;23(6):666-77. doi: 10.1016/j.chembiol.2016.05.011. Epub 2016 Jun 16.

17.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O'Donnell MR, Mlisana KP, Wortman J, Birren BW, Grosset J, Earl AM, Pym AS.

Nat Genet. 2016 May;48(5):544-51. doi: 10.1038/ng.3548. Epub 2016 Apr 11.

18.

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.

Malinga LA, Abeel T, Desjardins CA, Dlamini TC, Cassell G, Chapman SB, Birren BW, Earl AM, van der Walt M.

Genome Announc. 2016 Mar 3;4(2). pii: e01771-15. doi: 10.1128/genomeA.01771-15.

19.

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.

Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR.

PLoS Negl Trop Dis. 2016 Jan 11;10(1):e0004332. doi: 10.1371/journal.pntd.0004332. eCollection 2016 Jan.

20.

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.

Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA.

PLoS Genet. 2015 Oct 6;11(10):e1005493. doi: 10.1371/journal.pgen.1005493. eCollection 2015 Oct.

21.

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.

Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O'Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM.

PLoS Med. 2015 Sep 29;12(9):e1001880. doi: 10.1371/journal.pmed.1001880. eCollection 2015 Sep.

22.

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.

Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA.

MBio. 2015 Sep 1;6(5):e00868-15. doi: 10.1128/mBio.00868-15.

23.

MEF2D deficiency in neonatal cardiomyocytes triggers cell cycle re-entry and programmed cell death in vitro.

Estrella NL, Clark AL, Desjardins CA, Nocco SE, Naya FJ.

J Biol Chem. 2015 Oct 2;290(40):24367-80. doi: 10.1074/jbc.M115.666461. Epub 2015 Aug 20.

24.

Epidemiologic Investigation of a Cluster of Neuroinvasive Bacillus cereus Infections in 5 Patients With Acute Myelogenous Leukemia.

Rhee C, Klompas M, Tamburini FB, Fremin BJ, Chea N, Epstein L, Halpin AL, Guh A, Gallen R, Coulliette A, Gee J, Hsieh C, Desjardins CA, Pedamullu CS, DeAngelo DJ, Manzo VE, Folkerth RD, Milner DA Jr, Pecora N, Osborne M, Chalifoux-Judge D, Bhatt AS, Yokoe DS.

Open Forum Infect Dis. 2015 Jul 1;2(3):ofv096. doi: 10.1093/ofid/ofv096. eCollection 2015 Sep.

25.

Correction: EGR1 functions as a potent repressor of MEF2 transcriptional activity.

Feng Y, Desjardins CA, Cooper O, Kontor A, Nocco SE, Naya FJ.

PLoS One. 2015 Jun 24;10(6):e0131619. doi: 10.1371/journal.pone.0131619. eCollection 2015. No abstract available.

26.

EGR1 Functions as a Potent Repressor of MEF2 Transcriptional Activity.

Feng Y, Desjardins CA, Cooper O, Kontor A, Nocco SE, Naya FJ.

PLoS One. 2015 May 26;10(5):e0127641. doi: 10.1371/journal.pone.0127641. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131619.

27.

Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing.

Williams OM, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, Desjardins CA, Banerjee A, Drobniewski F, Earl AM, Cooke GS.

Emerg Infect Dis. 2015 Jun;21(6):1082-4. doi: 10.3201/eid2106.141903. No abstract available.

28.

Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.

Desjardins CA, Sanscrainte ND, Goldberg JM, Heiman D, Young S, Zeng Q, Madhani HD, Becnel JJ, Cuomo CA.

Nat Commun. 2015 May 13;6:7121. doi: 10.1038/ncomms8121.

29.

MEF2 transcription factors regulate distinct gene programs in mammalian skeletal muscle differentiation.

Estrella NL, Desjardins CA, Nocco SE, Clark AL, Maksimenko Y, Naya FJ.

J Biol Chem. 2015 Jan 9;290(2):1256-68. doi: 10.1074/jbc.M114.589838. Epub 2014 Nov 21.

30.

Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.

Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER.

PLoS Pathog. 2014 Jun 19;10(6):e1004200. doi: 10.1371/journal.ppat.1004200. eCollection 2014 Jun. Erratum in: PLoS Pathog. 2014 Aug;10(8):e1004371. Dunbar, Tiffany A [corrected to Dunbar, Tiffany L].

31.

Chronic treatment with novel small molecule Hsp90 inhibitors rescues striatal dopamine levels but not α-synuclein-induced neuronal cell loss.

McFarland NR, Dimant H, Kibuuka L, Ebrahimi-Fakhari D, Desjardins CA, Danzer KM, Danzer M, Fan Z, Schwarzschild MA, Hirst W, McLean PJ.

PLoS One. 2014 Jan 20;9(1):e86048. doi: 10.1371/journal.pone.0086048. eCollection 2014.

32.

Staphylococcal enterotoxin P predicts bacteremia in hospitalized patients colonized with methicillin-resistant Staphylococcus aureus.

Calderwood MS, Desjardins CA, Sakoulas G, Nicol R, Dubois A, Delaney ML, Kleinman K, Cosimi LA, Feldgarden M, Onderdonk AB, Birren BW, Platt R, Huang SS; CDC Prevention Epicenters Program.

J Infect Dis. 2014 Feb 15;209(4):571-7. doi: 10.1093/infdis/jit501. Epub 2013 Sep 16.

33.

Evolutionary dynamics of the accessory genome of Listeria monocytogenes.

den Bakker HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q, Young SK, Kodira CD, Yandava C, Hepburn TA, Haas BJ, Birren BW, Wiedmann M.

PLoS One. 2013 Jun 25;8(6):e67511. doi: 10.1371/journal.pone.0067511. Print 2013.

34.

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.

Desjardins CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB.

Nat Genet. 2013 May;45(5):495-500. doi: 10.1038/ng.2585. Epub 2013 Mar 24.

35.

Postmortem brain levels of urate and precursors in Parkinson's disease and related disorders.

McFarland NR, Burdett T, Desjardins CA, Frosch MP, Schwarzschild MA.

Neurodegener Dis. 2013;12(4):189-98. doi: 10.1159/000346370. Epub 2013 Feb 28.

36.

Fine-scale mapping of the Nasonia genome to chromosomes using a high-density genotyping microarray.

Desjardins CA, Gadau J, Lopez JA, Niehuis O, Avery AR, Loehlin DW, Richards S, Colbourne JK, Werren JH.

G3 (Bethesda). 2013 Feb;3(2):205-15. doi: 10.1534/g3.112.004739. Epub 2013 Feb 1.

37.

Disrupted and transgenic urate oxidase alter urate and dopaminergic neurodegeneration.

Chen X, Burdett TC, Desjardins CA, Logan R, Cipriani S, Xu Y, Schwarzschild MA.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):300-5. doi: 10.1073/pnas.1217296110. Epub 2012 Dec 17.

38.

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.

Cuomo CA, Desjardins CA, Bakowski MA, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER.

Genome Res. 2012 Dec;22(12):2478-88. doi: 10.1101/gr.142802.112. Epub 2012 Jul 18.

39.

High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).

Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC, Carr J, Posey J, Butler WR.

Stand Genomic Sci. 2011 Dec 31;5(3):389-97. doi: 10.4056/sigs.2255041. Epub 2011 Dec 30.

40.

Efficient determination of purine metabolites in brain tissue and serum by high-performance liquid chromatography with electrochemical and UV detection.

Burdett TC, Desjardins CA, Logan R, McFarland NR, Chen X, Schwarzschild MA.

Biomed Chromatogr. 2013 Jan;27(1):122-9. doi: 10.1002/bmc.2760. Epub 2012 Jun 5.

PMID:
22674671
41.

Protection of dopaminergic cells by urate requires its accumulation in astrocytes.

Cipriani S, Desjardins CA, Burdett TC, Xu Y, Xu K, Schwarzschild MA.

J Neurochem. 2012 Oct;123(1):172-81. doi: 10.1111/j.1471-4159.2012.07820.x. Epub 2012 Aug 22.

42.

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.

Kos VN, Desjardins CA, Griggs A, Cerqueira G, Van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J, Feldgarden M, Lawley T, Gill SR, Haas BJ, Birren B, Gilmore MS.

MBio. 2012 May 22;3(3). pii: e00112-12. doi: 10.1128/mBio.00112-12. Print 2012.

43.

Urate and its transgenic depletion modulate neuronal vulnerability in a cellular model of Parkinson's disease.

Cipriani S, Desjardins CA, Burdett TC, Xu Y, Xu K, Schwarzschild MA.

PLoS One. 2012;7(5):e37331. doi: 10.1371/journal.pone.0037331. Epub 2012 May 14.

44.

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CM, Birren BW, Cuomo CA.

PLoS Genet. 2011 Oct;7(10):e1002345. doi: 10.1371/journal.pgen.1002345. Epub 2011 Oct 27.

45.

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.

Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach AL, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW, Sinskey AJ.

PLoS Genet. 2011 Sep;7(9):e1002219. doi: 10.1371/journal.pgen.1002219. Epub 2011 Sep 8.

46.

Comparative functional genomics of the fission yeasts.

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

47.

The mushroom habitat as an ecological arena for global exchange of Wolbachia.

Stahlhut JK, Desjardins CA, Clark ME, Baldo L, Russell JA, Werren JH, Jaenike J.

Mol Ecol. 2010 May;19(9):1940-52. doi: 10.1111/j.1365-294X.2010.04572.x.

PMID:
20529071
48.

Data mining cDNAs reveals three new single stranded RNA viruses in Nasonia (Hymenoptera: Pteromalidae).

Oliveira DC, Hunter WB, Ng J, Desjardins CA, Dang PM, Werren JH.

Insect Mol Biol. 2010 Feb;19 Suppl 1:99-107. doi: 10.1111/j.1365-2583.2009.00934.x.

49.

Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias.

Behura SK, Stanke M, Desjardins CA, Werren JH, Severson DW.

Insect Mol Biol. 2010 Feb;19 Suppl 1:49-58. doi: 10.1111/j.1365-2583.2009.00933.x.

50.

Insights into the venom composition of the ectoparasitoid wasp Nasonia vitripennis from bioinformatic and proteomic studies.

de Graaf DC, Aerts M, Brunain M, Desjardins CA, Jacobs FJ, Werren JH, Devreese B.

Insect Mol Biol. 2010 Feb;19 Suppl 1:11-26. doi: 10.1111/j.1365-2583.2009.00914.x.

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